Hello,
I had carried out a 20ns protein simulation on Gromacs v3.2.1. Later I
continued the simulation on Gromacs v3.3.
I ran the following command supplying the energy file and trajectory
file. But the program gave error and stopped (log message is given below).
Since I read that supply of energy file is not absolutely required. I
again ran tpbconv without -e option for another 10ns. This time the
program ran with the warning message that the continuation will not be
exact.
"WARNING: The simulation uses pressure and/or Nose-Hoover temperature
coupling,
the continuation will only be exact when an energy file is
supplied".
When I plotted the trajectory of the Potential energy, I found the
difference, with PE much below than the previous simulation (PE dropped
from -559000 to -561000). Can I use the data of this additional
simulation, or is it a drastic variation, that I need to take care of?
Thank you,
expecting your suggessions.
######################################################################################
[EMAIL PROTECTED] TRAJEC_WT]$ tpbconv -s
../OTHERS_WT/b4md_1cyp_WT.tpr -f rerereafter15_WT.trr -e
../OTHERS_WT/rerereafter15_WT.edr -o new.tpr -until 30000
:-) G R O M A C S (-:
Gromacs Runs On Most of All Computer Systems
:-) VERSION 3.3 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2004, The GROMACS development team,
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) tpbconv (-:
Option Filename Type Description
------------------------------------------------------------
-s ../OTHERS_WT/b4md_1cyp_WT.tpr Input Generic run input: tpr tpb
tpa xml
-f rerereafter15_WT.trr Input, Opt! Full precision trajectory: trr trj
-e ../OTHERS_WT/rerereafter15_WT.edr Input, Opt! Generic energy: edr ene
-n index.ndx Input, Opt. Index file
-o new.tpr Output Generic run input: tpr tpb tpa xml
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]X bool no Use dialog box GUI to edit command line options
-nice int 0 Set the nicelevel
-time real -1 Continue from frame at this time (ps) instead of
the last frame
-extend real 0 Extend runtime by this amount (ps)
-until real 30000 Extend runtime until this ending time (ps)
-[no]zeroq bool no Set the charges of a group (from the index) to
zero
-[no]unconstrained
bool yes For a continuous trajectory, the constraints
should not be solved before the first step
(default)
Reading toplogy and shit from ../OTHERS_WT/b4md_1cyp_WT.tpr
Reading file ../OTHERS_WT/b4md_1cyp_WT.tpr, VERSION 3.1.4 (single precision)
Note: tpx file_version 24, software version 40
Note: nLincsIter not in run input file, setting it to 1
Modifying ir->bUncStart to TRUE
READING COORDS, VELS AND BOX FROM TRAJECTORY rerereafter15_WT.trr...
trn version: GMX_trn_file (single precision)
Read frame 684: step 341344 time 20000.000
Using frame of step 341344 time 20000
Opened ../OTHERS_WT/rerereafter15_WT.edr as single precision energy file
Reading frame 60 time 19917.312
-------------------------------------------------------
Program tpbconv, VERSION 3.3
Source code file: enxio.c, line: 358
Fatal error:
Could not find energy term named 'Pcoupl-Mu-XX'
-------------------------------------------------------
"Stop Drinking My Beer !" (The Amps)
#########################################################################################
--
Sridhar Acharya, M
Senior Research Fellow
Lab of Computational Biology
CDFD, Gandipet Campus
Hyderabad. AP. INDIA
http://www.cdfd.org.in
email: [EMAIL PROTECTED]
Phone: Lab: 08413-235467*2044
Mobile: 9866147193
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email;internet:[EMAIL PROTECTED]
title:Senior Research Fellow
tel;work:08413-235467*2044
tel;home:040-27505833
tel;cell:9866147193
x-mozilla-html:TRUE
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